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- PDB-9n4i: YehD receptor binding domain Y150A -

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Basic information

Entry
Database: PDB / ID: 9n4i
TitleYehD receptor binding domain Y150A
ComponentsYehD protein
KeywordsCELL ADHESION / Adhesin / CUP pili
Function / homologyUncharacterised conserved protein UCP030811 / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / cell adhesion involved in single-species biofilm formation / Adhesion domain superfamily / pilus / Uncharacterized fimbrial-like protein YehA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsTamadonfar, K.O. / Klein, R.D. / Hultgren, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI048689 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI029549 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007172-40 United States
CitationJournal: To Be Published
Title: The Yeh pilus, tipped by an adhesin equipped with a mobile alpha-helical flap motif, mediates GI colonization via pectin adherence.
Authors: Tamadonfar, K.O. / Klein, R.D. / Lopatto, E. / Zimmerman, M.I. / Azimzadeh, P. / Porter, J. / Bazan Villicana, J. / Pinkner, J.S. / Birchenough, G. / Dodson, K.W. / Bowman, G.R. / Hultgren, S.J.
History
DepositionFeb 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YehD protein
B: YehD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6404
Polymers36,4562
Non-polymers1842
Water1,11762
1
A: YehD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4123
Polymers18,2281
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YehD protein


Theoretical massNumber of molelcules
Total (without water)18,2281
Polymers18,2281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.351, 31.613, 87.873
Angle α, β, γ (deg.)90.00, 93.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YehD protein


Mass: 18228.135 Da / Num. of mol.: 2 / Fragment: Receptor Binding Domain / Mutation: Y150A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P33340
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NaAcetate, 0.1 M Tris 8.8, and ~20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072157 Å
DetectorType: NOIR-1 / Detector: CMOS / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072157 Å / Relative weight: 1
ReflectionResolution: 1.68→39.2 Å / Num. obs: 46949 / % possible obs: 92.86 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1095 / Rrim(I) all: 0.1298 / Net I/σ(I): 8.85
Reflection shellResolution: 1.68→1.74 Å / Rmerge(I) obs: 1.426 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 16626 / CC1/2: 0.414 / Rrim(I) all: 1.682

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→39.2 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2572 2339 5.05 %
Rwork0.224 --
obs0.2257 46335 92.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 12 62 2628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122612
X-RAY DIFFRACTIONf_angle_d1.1133566
X-RAY DIFFRACTIONf_dihedral_angle_d10.6741540
X-RAY DIFFRACTIONf_chiral_restr0.061428
X-RAY DIFFRACTIONf_plane_restr0.007458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.71430.33431410.30972419X-RAY DIFFRACTION89
1.7143-1.75160.36971400.30582487X-RAY DIFFRACTION89
1.7516-1.79230.30471100.28772580X-RAY DIFFRACTION93
1.7923-1.83720.27671150.2662563X-RAY DIFFRACTION92
1.8372-1.88680.29461420.25652599X-RAY DIFFRACTION96
1.8868-1.94240.29441350.25542672X-RAY DIFFRACTION96
1.9424-2.0050.28691640.22932651X-RAY DIFFRACTION96
2.005-2.07670.26281550.23792648X-RAY DIFFRACTION96
2.0767-2.15990.25151310.21992648X-RAY DIFFRACTION96
2.1599-2.25810.27131410.21342622X-RAY DIFFRACTION94
2.2581-2.37720.21291430.2232665X-RAY DIFFRACTION97
2.3772-2.52610.26391030.23932633X-RAY DIFFRACTION93
2.5261-2.72110.29321510.24062574X-RAY DIFFRACTION93
2.7211-2.99490.2671340.24272572X-RAY DIFFRACTION92
2.9949-3.42810.27791380.22332506X-RAY DIFFRACTION89
3.4281-4.31850.23651290.19412405X-RAY DIFFRACTION85
4.3185-39.20.20221670.18512752X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 20.3817 Å / Origin y: -0.6892 Å / Origin z: 19.825 Å
111213212223313233
T0.1771 Å20.018 Å20.0214 Å2-0.1216 Å20.0221 Å2--0.1813 Å2
L0.548 °20.0242 °20.758 °2--0.0156 °20.0111 °2--1.0862 °2
S-0.0355 Å °-0.0801 Å °0.0321 Å °0.0339 Å °0.0199 Å °0.0395 Å °-0.0138 Å °-0.1336 Å °0.0088 Å °
Refinement TLS groupSelection details: all

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